Just read that thread fully, from the first post to the last. You'll find full description of OTA update process and the point of minimal changes for disrupting it only without affecting any other processes. While it was tested on Kindle Touch, there is no difference between PW and KT in this aspect. Or you can disprove this statement by your experience after trying it (I'm certainly interested in testimonials).

I did read it (again) today and I did notice something that would probably explain both the comment about error code 003 and the above posted experiences.

As far as I can see (without actual testing) is that the described method only interferes with the in-system updater.

It would not interfere with the other ('auto-pilot') updater in the initramfs.
That updater has its own certificate storage (in the initramfs) which our (MR) certificate addition does not affect.

It is the 'auto-pilot' updater that generates the E003 code when people try to install our packages by re-starting (or re-booting) the Kindle instead of using the home -> menu -> settings -> menu -> update Kindle proceedure.

O.P: Check your notes - see if the downloaded updates where executed on a re-start or re-boot.

I.E: the only way to prevent the forced update is to either prevent the *.bin from showing up on /mnt/us or detecting it and moving/re-moving it early in the shut-down sequence.